When I first saw it, just like with the Ben Stein one from Ferris Buller and Bill Paxton from Twister, they CGI's their current face with the older and did it that way. The old Trek sets are junked. And Shatner has aged 15 years since Trek VI. Not to mention how much Ben Stein looked in his commercial.
Saw on TVGuide.com that Shater said he was "CGI'd" into it.